1 Summary

1.1 Groups information

mae <- get(load("hg38_gcimp_mae.rda"))
mae
## A MultiAssayExperiment object of 2 listed
##  experiments with user-defined names and respective classes.
##  Containing an ExperimentList class object of length 2:
##  [1] DNA methylation: RangedSummarizedExperiment with 135374 rows and 244 columns
##  [2] Gene expression: RangedSummarizedExperiment with 57035 rows and 244 columns
## Features:
##  experiments() - obtain the ExperimentList instance
##  colData() - the primary/phenotype DataFrame
##  sampleMap() - the sample availability DataFrame
##  `$`, `[`, `[[` - extract colData columns, subset, or experiment
##  *Format() - convert into a long or wide DataFrame
##  assays() - convert ExperimentList to a SimpleList of matrices
samples.info <- SummarizedExperiment::colData(mae)
plyr::count(samples.info$subtype_Supervised.DNA.Methylation.Cluster)

1.2 Samples

1.3 Arguments

1.4 Summary results

1.4.1 Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2 Glioma analysis: G-CIMP-high vs G-CIMP-low

2.1 Probes hypermethylated in G-CIMP-high vs G-CIMP-low

Volcano plot - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

Volcano plot - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.1 Significant anti-correlated pairs of gene-probes

Heatmap: hypomethylated paired probes

Heatmap: hypomethylated paired probes

2.1.1.1 Statehub: Chromatin state evaluation

The plot below was produced with funciVar tool (https://github.com/Simon-Coetzee/funcivar), which calculate overlaps and enrichment between genomic variants and genomic features or segmentations. The segmentations used were retrieved from (http://statehub.org/).
Funcivar: hypermethylated paired probes. Produced with funciVar tool (https://github.com/Simon-Coetzee/funcivar) and statehub.org data.

Funcivar: hypermethylated paired probes. Produced with funciVar tool (https://github.com/Simon-Coetzee/funcivar) and statehub.org data.

2.1.2 Motif enrichment analysis

Probes hypermethylated in G-CIMP-high vs G-CIMP-low

Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3 TF analysis

2.1.3.1 Top potential TF

The table below shows for a given enriched motif, the top potential TF (best ranked TF based on the p-value) belonging to the same family or subfamily (TFClass classification) of the TF motif. The columns with a prefix p-value shows how significant is the anti-correlation of the average DNA methylation level of probes with the given motif and the TF expression.

2.1.3.2 potential TF family

The table below shows for a given enriched motif, all potential TF belonging to the same family (TFClass classification) of the TF motif. The columns with a prefix p-value shows how significant is the anti-correlation of the average DNA methylation level of probes with the given motif and the TF expression.

2.1.3.3 potential TF subfamily

The table below shows for a given enriched motif, all potential TF belonging to the same subfamily (TFClass classification) of the TF motif. The columns with a prefix p-value shows how significant is the anti-correlation of the average DNA methylation level of probes with the given motif and the TF expression.

2.1.3.4 TF plots

2.1.3.4.1 TF plots

The plot below shows for a given enriched motif the ranking of p-values showing how significant is the anti-correlation of the average DNA methylation level of probes with the given motif and the TF expression. TFs in the same family and subfamily of the given TF motif are highlighted. Also, the top 3 TFs (lowest p-values) are highlighted.

2.1.3.4.1.1 LHX2
LHX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

LHX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.2 PO6F2
PO6F2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

PO6F2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.3 RX
RX - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

RX - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.4 JUNB
JUNB - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

JUNB - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.5 GBX2
GBX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

GBX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.6 NOTO
NOTO - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NOTO - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.7 DLX3
DLX3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

DLX3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.8 SOX10
SOX10 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX10 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.9 MIXL1
MIXL1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

MIXL1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.10 SIX2
SIX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SIX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.11 LBX2
LBX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

LBX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.12 BATF
BATF - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

BATF - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.13 EVX1
EVX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

EVX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.14 ZBT49
ZBT49 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

ZBT49 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.15 SIX1
SIX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SIX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.16 SOX4
SOX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.17 DLX2
DLX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

DLX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.18 FOXQ1
FOXQ1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXQ1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.19 SOX9
SOX9 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX9 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.20 HXB3
HXB3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HXB3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.21 DLX5
DLX5 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

DLX5 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.22 HXD3
HXD3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HXD3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.23 LHX9
LHX9 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

LHX9 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.24 VAX2
VAX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

VAX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.25 EMX2
EMX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

EMX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.26 PAX4
PAX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

PAX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.27 GBX1
GBX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

GBX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.28 FOSB
FOSB - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOSB - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.29 JUND
JUND - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

JUND - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.30 JUN
JUN - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

JUN - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.31 SOX13
SOX13 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX13 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.32 TWST1
TWST1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

TWST1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.33 HME2
HME2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HME2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.34 FOSL2
FOSL2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOSL2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.35 ELF3
ELF3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

ELF3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.36 NKX61
NKX61 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NKX61 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.37 SOX2
SOX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.38 NFIA
NFIA - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NFIA - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.39 SOX10
SOX10 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX10 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.40 BARX1
BARX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

BARX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.41 EMX1
EMX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

EMX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.42 HXA2
HXA2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HXA2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.43 DLX4
DLX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

DLX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.44 NF2L2
NF2L2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NF2L2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.45 BACH2
BACH2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

BACH2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.46 PO4F2
PO4F2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

PO4F2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.47 ATF2
ATF2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

ATF2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.48 TEAD2
TEAD2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

TEAD2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.49 FOXC2
FOXC2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXC2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.50 VSX2
VSX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

VSX2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.51 CEBPA
CEBPA - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

CEBPA - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.52 SOX9
SOX9 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX9 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.53 EHF
EHF - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

EHF - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.54 FOS
FOS - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOS - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.55 SOX3
SOX3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX3 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.56 NFE2
NFE2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NFE2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.57 NKX62
NKX62 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NKX62 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.58 HXA13
HXA13 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HXA13 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.59 SOX18
SOX18 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX18 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.60 OLIG2
OLIG2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

OLIG2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.61 NOBOX
NOBOX - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

NOBOX - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.62 LHX4
LHX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

LHX4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.63 CUX1
CUX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

CUX1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.64 HLTF
HLTF - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HLTF - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.65 LMX1A
LMX1A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

LMX1A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.66 VEZF1
VEZF1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

VEZF1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.67 BHE23
BHE23 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

BHE23 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.68 FOSL1
FOSL1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOSL1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.69 MYF6
MYF6 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

MYF6 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.70 SMAD2
SMAD2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SMAD2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.71 FOXH1
FOXH1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXH1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.72 FOXC1
FOXC1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXC1 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.73 ETS2
ETS2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

ETS2 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.1.74 SMAD4
SMAD4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SMAD4 - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2 Scatter plot

The plot below shows for a given enriched motif the average DNA methylation level of probes with the signature for the given motif vs the TF expression. Each dot is a sample.

2.1.3.4.2.1 top 3 expression vs avg DNA methylation of paired enriched probes for LHX2
top3 TF expression vs avg DNA methylation of paired enriched probes for LHX2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for LHX2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.2 top 3 expression vs avg DNA methylation of paired enriched probes for PO6F2
top3 TF expression vs avg DNA methylation of paired enriched probes for PO6F2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for PO6F2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.3 top 3 expression vs avg DNA methylation of paired enriched probes for RX
top3 TF expression vs avg DNA methylation of paired enriched probes for RX_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for RX_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.4 top 3 expression vs avg DNA methylation of paired enriched probes for JUNB
top3 TF expression vs avg DNA methylation of paired enriched probes for JUNB_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for JUNB_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.5 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for GBX2
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for GBX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for GBX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.6 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for NOTO
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for NOTO_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for NOTO_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.7 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for DLX3
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX3_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX3_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.8 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX10
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX10_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX10_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.9 top 3 expression vs avg DNA methylation of paired enriched probes for MIXL1
top3 TF expression vs avg DNA methylation of paired enriched probes for MIXL1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for MIXL1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.10 top 3 expression vs avg DNA methylation of paired enriched probes for SIX2
top3 TF expression vs avg DNA methylation of paired enriched probes for SIX2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for SIX2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.11 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for LBX2
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for LBX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for LBX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.12 top 3 expression vs avg DNA methylation of paired enriched probes for BATF
top3 TF expression vs avg DNA methylation of paired enriched probes for BATF_HUMAN.H11MO.1.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for BATF_HUMAN.H11MO.1.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.13 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for EVX1
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for EVX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for EVX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.14 ZSCAN16 and top 3 expression vs avg DNA methylation of paired enriched probes for ZBT49
ZSCAN16 and top3 TF expression vs avg DNA methylation of paired enriched probes for ZBT49_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

ZSCAN16 and top3 TF expression vs avg DNA methylation of paired enriched probes for ZBT49_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.15 top 3 expression vs avg DNA methylation of paired enriched probes for SIX1
top3 TF expression vs avg DNA methylation of paired enriched probes for SIX1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for SIX1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.16 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX4
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX4_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX4_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.17 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for DLX2
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.18 FOXM1 and top 3 expression vs avg DNA methylation of paired enriched probes for FOXQ1
FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXQ1_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXQ1_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.19 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX9
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX9_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX9_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.20 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for HXB3
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXB3_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXB3_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.21 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for DLX5
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX5_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX5_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.22 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for HXD3
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXD3_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXD3_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.23 top 3 expression vs avg DNA methylation of paired enriched probes for LHX9
top3 TF expression vs avg DNA methylation of paired enriched probes for LHX9_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for LHX9_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.24 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for VAX2
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for VAX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for VAX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.25 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for EMX2
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for EMX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for EMX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.26 PAX3 and top 3 expression vs avg DNA methylation of paired enriched probes for PAX4
PAX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for PAX4_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

PAX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for PAX4_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.27 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for GBX1
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for GBX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for GBX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.28 top 3 expression vs avg DNA methylation of paired enriched probes for FOSB
top3 TF expression vs avg DNA methylation of paired enriched probes for FOSB_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for FOSB_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.29 top 3 expression vs avg DNA methylation of paired enriched probes for JUND
top3 TF expression vs avg DNA methylation of paired enriched probes for JUND_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for JUND_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.30 top 3 expression vs avg DNA methylation of paired enriched probes for JUN
top3 TF expression vs avg DNA methylation of paired enriched probes for JUN_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for JUN_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.31 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX13
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX13_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX13_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.32 top 3 expression vs avg DNA methylation of paired enriched probes for TWST1
top3 TF expression vs avg DNA methylation of paired enriched probes for TWST1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for TWST1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.33 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for HME2
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for HME2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for HME2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.34 top 3 expression vs avg DNA methylation of paired enriched probes for FOSL2
top3 TF expression vs avg DNA methylation of paired enriched probes for FOSL2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for FOSL2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.35 top 3 expression vs avg DNA methylation of paired enriched probes for ELF3
top3 TF expression vs avg DNA methylation of paired enriched probes for ELF3_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for ELF3_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.36 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for NKX61
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for NKX61_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for NKX61_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.37 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX2
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.38 top 3 expression vs avg DNA methylation of paired enriched probes for NFIA
top3 TF expression vs avg DNA methylation of paired enriched probes for NFIA_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for NFIA_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.39 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX10
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX10_HUMAN.H11MO.1.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX10_HUMAN.H11MO.1.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.40 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for BARX1
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for BARX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for BARX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.41 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for EMX1
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for EMX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for EMX1_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.42 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for HXA2
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXA2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXA2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.43 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for DLX4
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX4_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for DLX4_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.44 top 3 expression vs avg DNA methylation of paired enriched probes for NF2L2
top3 TF expression vs avg DNA methylation of paired enriched probes for NF2L2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for NF2L2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.45 top 3 expression vs avg DNA methylation of paired enriched probes for BACH2
top3 TF expression vs avg DNA methylation of paired enriched probes for BACH2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for BACH2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.46 top 3 expression vs avg DNA methylation of paired enriched probes for PO4F2
top3 TF expression vs avg DNA methylation of paired enriched probes for PO4F2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for PO4F2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.47 top 3 expression vs avg DNA methylation of paired enriched probes for ATF2
top3 TF expression vs avg DNA methylation of paired enriched probes for ATF2_HUMAN.H11MO.1.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for ATF2_HUMAN.H11MO.1.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.48 top 3 expression vs avg DNA methylation of paired enriched probes for TEAD2
top3 TF expression vs avg DNA methylation of paired enriched probes for TEAD2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for TEAD2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.49 FOXM1 and top 3 expression vs avg DNA methylation of paired enriched probes for FOXC2
FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXC2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXC2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.50 top 3 expression vs avg DNA methylation of paired enriched probes for VSX2
top3 TF expression vs avg DNA methylation of paired enriched probes for VSX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for VSX2_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.51 top 3 expression vs avg DNA methylation of paired enriched probes for CEBPA
top3 TF expression vs avg DNA methylation of paired enriched probes for CEBPA_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for CEBPA_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.52 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX9
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX9_HUMAN.H11MO.1.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX9_HUMAN.H11MO.1.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.53 top 3 expression vs avg DNA methylation of paired enriched probes for EHF
top3 TF expression vs avg DNA methylation of paired enriched probes for EHF_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for EHF_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.54 top 3 expression vs avg DNA methylation of paired enriched probes for FOS
top3 TF expression vs avg DNA methylation of paired enriched probes for FOS_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for FOS_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.55 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX3
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX3_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX3_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.56 top 3 expression vs avg DNA methylation of paired enriched probes for NFE2
top3 TF expression vs avg DNA methylation of paired enriched probes for NFE2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for NFE2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.57 HMX3 and top 3 expression vs avg DNA methylation of paired enriched probes for NKX62
HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for NKX62_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HMX3 and top3 TF expression vs avg DNA methylation of paired enriched probes for NKX62_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.58 HOXD13 and top 3 expression vs avg DNA methylation of paired enriched probes for HXA13
HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXA13_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

HOXD13 and top3 TF expression vs avg DNA methylation of paired enriched probes for HXA13_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.59 SOX11 and top 3 expression vs avg DNA methylation of paired enriched probes for SOX18
SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX18_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

SOX11 and top3 TF expression vs avg DNA methylation of paired enriched probes for SOX18_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.60 top 3 expression vs avg DNA methylation of paired enriched probes for OLIG2
top3 TF expression vs avg DNA methylation of paired enriched probes for OLIG2_HUMAN.H11MO.1.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for OLIG2_HUMAN.H11MO.1.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.61 top 3 expression vs avg DNA methylation of paired enriched probes for NOBOX
top3 TF expression vs avg DNA methylation of paired enriched probes for NOBOX_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for NOBOX_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.62 top 3 expression vs avg DNA methylation of paired enriched probes for LHX4
top3 TF expression vs avg DNA methylation of paired enriched probes for LHX4_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for LHX4_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.63 top 3 expression vs avg DNA methylation of paired enriched probes for CUX1
top3 TF expression vs avg DNA methylation of paired enriched probes for CUX1_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for CUX1_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.64 top 3 expression vs avg DNA methylation of paired enriched probes for HLTF
top3 TF expression vs avg DNA methylation of paired enriched probes for HLTF_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for HLTF_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.65 top 3 expression vs avg DNA methylation of paired enriched probes for LMX1A
top3 TF expression vs avg DNA methylation of paired enriched probes for LMX1A_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for LMX1A_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.66 top 3 expression vs avg DNA methylation of paired enriched probes for VEZF1
top3 TF expression vs avg DNA methylation of paired enriched probes for VEZF1_HUMAN.H11MO.1.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for VEZF1_HUMAN.H11MO.1.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.67 top 3 expression vs avg DNA methylation of paired enriched probes for BHE23
top3 TF expression vs avg DNA methylation of paired enriched probes for BHE23_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for BHE23_HUMAN.H11MO.0.D - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.68 top 3 expression vs avg DNA methylation of paired enriched probes for FOSL1
top3 TF expression vs avg DNA methylation of paired enriched probes for FOSL1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for FOSL1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.69 top 3 expression vs avg DNA methylation of paired enriched probes for MYF6
top3 TF expression vs avg DNA methylation of paired enriched probes for MYF6_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for MYF6_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.70 top 3 expression vs avg DNA methylation of paired enriched probes for SMAD2
top3 TF expression vs avg DNA methylation of paired enriched probes for SMAD2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for SMAD2_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.71 FOXM1 and top 3 expression vs avg DNA methylation of paired enriched probes for FOXH1
FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXH1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXH1_HUMAN.H11MO.0.A - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.72 FOXM1 and top 3 expression vs avg DNA methylation of paired enriched probes for FOXC1
FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXC1_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

FOXM1 and top3 TF expression vs avg DNA methylation of paired enriched probes for FOXC1_HUMAN.H11MO.0.C - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.73 top 3 expression vs avg DNA methylation of paired enriched probes for ETS2
top3 TF expression vs avg DNA methylation of paired enriched probes for ETS2_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for ETS2_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.1.3.4.2.74 top 3 expression vs avg DNA methylation of paired enriched probes for SMAD4
top3 TF expression vs avg DNA methylation of paired enriched probes for SMAD4_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

top3 TF expression vs avg DNA methylation of paired enriched probes for SMAD4_HUMAN.H11MO.0.B - Probes hypermethylated in G-CIMP-high vs G-CIMP-low

2.2 Probes hypomethylated in G-CIMP-high vs G-CIMP-low

Volcano plot - Probes hypomethylated in G-CIMP-high vs G-CIMP-low

Volcano plot - Probes hypomethylated in G-CIMP-high vs G-CIMP-low

3 Code

library(stringr)
library(TCGAbiolinks)
library(dplyr)
library(ELMER)
library(parallel)
#-----------------------------------
# 1 - Identify Samples
# ----------------------------------
gcimp.samples <- TCGAquery_subtype("lgg.gbm") %>% filter(base::grepl("G-CIMP",Supervised.DNA.Methylation.Cluster,ignore.case = T))
gcimp.low.samples <- gcimp.samples %>% filter(base::grepl("G-CIMP-low",Supervised.DNA.Methylation.Cluster, ignore.case = T))
gcimp.high.samples <- gcimp.samples %>% filter(base::grepl("G-CIMP-high",Supervised.DNA.Methylation.Cluster, ignore.case = T))

msg <- paste0("-----------------------------------------------\n",
              "GCIMP samples ", nrow(gcimp.samples),"\n",
              "GCIMP Low samples ", nrow(gcimp.low.samples),"\n",
              "GCIMP High samples ", nrow(gcimp.high.samples),"\n",
              "-----------------------------------------------")
message(msg)
#-----------------------------------
# 2 - Get data
# ----------------------------------
#-----------------------------------
# 2.1 - DNA Methylation
# ----------------------------------
for(cancer in c("LGG","GBM")){
  query <- GDCquery(project = paste0("TCGA-",toupper(cancer)),
                    data.category = "DNA Methylation",
                    sample.type = "Primary solid Tumor",
                    platform = "Illumina Human Methylation 450",
                    barcode =  gcimp.samples$patient)
  tryCatch({
    GDCdownload(query, chunks.per.download = 20)
  }, error = function(e) {
    GDCdownload(query, chunks.per.download = 5)
  })
  assign(tolower(cancer),GDCprepare(query, save = FALSE))
}
met <- SummarizedExperiment::cbind(lgg, gbm)
save(met, file = "gcimp_met.rda")
rm(lgg,gbm)
#-----------------------------------
# 2 - Expression
# ----------------------------------
for(cancer in c("LGG","GBM")){
  query <- GDCquery(project = paste0("TCGA-",toupper(cancer)),
                    data.category = "Transcriptome Profiling",
                    data.type = "Gene Expression Quantification",
                    workflow.type = "HTSeq - FPKM-UQ",
                    sample.type = "Primary solid Tumor",
                    barcode =  gcimp.samples$patient)
  tryCatch({
    GDCdownload(query, chunks.per.download = 20)
  }, error = function(e) {
    GDCdownload(query, chunks.per.download = 5)
  })
  assign(tolower(cancer), GDCprepare(query, save = FALSE))
}
exp <- SummarizedExperiment::cbind(lgg, gbm)
save(exp, file = "gcimp_exp.rda")
rm(lgg,gbm)

genome <- "hg38"
file <- "hg38_gcimp_mae.rda"
distal.probe <- get.feature.probe(genome = genome, met.platform = "450K",feature = NULL)
if(file.exists(file)) {
  mae <- get(load(file))
} else {
  mae <- createMAE(exp = "gcimp_exp.rda",
                   met = "gcimp_met.rda",
                   genome = genome,
                   met.platform = "450K",
                   linearize.exp = TRUE,   # Log2(exp + 1)
                   filter.probes = distal.probe,
                   TCGA = TRUE,
                   save = TRUE,
                   save.filename = file)
}
cores <- parallel::detectCores()/2
direction <- c("hyper","hypo")
group1 <- "G-CIMP-high"
group2 <- "G-CIMP-low"
group.col <- "subtype_Supervised.DNA.Methylation.Cluster"

for (j in direction){
  print(j)
  dir.out <- paste0("gcimp_high_vs_low_",genome,"/",j)
  dir.create(dir.out, recursive = TRUE)
  #--------------------------------------
  # STEP 3: Analysis                     |
  #--------------------------------------
  # Step 3.1: Get diff methylated probes |
  #--------------------------------------
  Sig.probes <- get.diff.meth(data       = mae,
                              group.col  = group.col,
                              group1     = group1,
                              group2     = group2,
                              minSubgroupFrac = 1,
                              cores      = cores,
                              dir.out    = dir.out,
                              diff.dir   = j,
                              pvalue     = 0.01)

  #-------------------------------------------------------------
  # Step 3.2: Identify significant probe-gene pairs            |
  #-------------------------------------------------------------
  # Collect nearby 20 genes for Sig.probes
  nearGenes <- GetNearGenes(data  = mae,
                            probe = Sig.probes$probe,
                            cores = cores)

  pair <- get.pair(data       = mae,
                   nearGenes  = nearGenes,
                   group.col  = group.col,
                   group1     = group1,
                   group2     = group2,
                   permu.dir  = paste0(dir.out,"/permu"),
                   dir.out    = dir.out,
                   diff.dir   = j,
                   minSubgroupFrac = 1,
                   cores      = cores,
                   mode       = "supervised",
                   label      = j,
                   permu.size = 10000,
                   raw.pvalue = 0.001)
  Sig.probes.paired <- unique(read.csv(paste0(dir.out,
                                              "/getPair.",j,
                                              ".pairs.significant.csv"),
                                       stringsAsFactors=FALSE)[,1])


  #-------------------------------------------------------------
  # Step 3.3: Motif enrichment analysis on the selected probes |
  #-------------------------------------------------------------
  if(length(Sig.probes.paired) > 10 ){
    #-------------------------------------------------------------
    # Step 3.3: Motif enrichment analysis on the selected probes |
    #-------------------------------------------------------------
    enriched.motif <- get.enriched.motif(probes  = Sig.probes.paired,
                                         dir.out = dir.out,
                                         data    = mae,
                                         label   = j)
    motif.enrichment <- read.csv(paste0(dir.out,
                                        "/getMotif.",j,
                                        ".motif.enrichment.csv"),
                                 stringsAsFactors=FALSE)
    if(length(enriched.motif) > 0){
      #-------------------------------------------------------------
      # Step 3.4: Identifying regulatory TFs                        |
      #-------------------------------------------------------------
      print("get.TFs")

      TF <- get.TFs(data           = mae,
                    enriched.motif = enriched.motif,
                    group.col      = group.col,
                    group1         = group1,
                    group2         = group2,
                    dir.out        = dir.out,
                    minSubgroupFrac = 1,
                    diff.dir       = j,
                    cores          = cores,
                    mode           = "supervised",
                    label          = j)
      TF.meth.cor <- get(load(paste0(dir.out,
                                     "/getTF.",j,
                                     ".TFs.with.motif.pvalue.rda")))
      save(mae,TF, enriched.motif, Sig.probes.paired,
           pair, nearGenes, Sig.probes, motif.enrichment,
           TF.meth.cor,
           file = paste0(dir.out,"/ELMER_results_",j,".rda"))
    }
  }
}
for (j in direction){
  print(j)
  dir.out <- paste0("gcimp_high_vs_low_",genome,"/",j)
  pairs <- readr::read_csv(file.path(file.path(dir.out,paste0("getPair.",j,".pairs.significant.csv"))))
  message("Scatter plots")
  scatter.plot(mae,
               byPair = list(probe = pairs$Probe, gene = pairs$GeneID),
               category = "subtype_Supervised.DNA.Methylation.Cluster",
               save = TRUE,
               lm_line = TRUE,
               dir.out = paste0(dir.out,"/significant_pairs_plot"))
  message("Schematic plot for probes")
  schematic.plot(data = mae,
                 group.col = "subtype_Supervised.DNA.Methylation.Cluster",
                 pair = pairs,
                 dir.out = paste0(dir.out,"/schematic_plots"),
                 save = TRUE,
                 byProbe = unique(pairs$Probe))
  message("Schematic plot for genes")
  # by gene ID and adding annotation tracks from StateHub               
  schematic.plot(data = mae,
                 group.col = "subtype_Supervised.DNA.Methylation.Cluster",
                 pair = pairs,
                 dir.out = dir.out,
                 save = TRUE,
                 byGeneID = unique(pairs$GeneID))
}

4 Session Information

## R version 3.4.3 (2017-11-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
##
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
##  [1] parallel  stats4    grid      stats     graphics  grDevices utils
##  [8] datasets  methods   base
##
## other attached packages:
##  [1] bindrcpp_0.2               GenomicRanges_1.30.1
##  [3] GenomeInfoDb_1.14.0        IRanges_2.12.0
##  [5] S4Vectors_0.16.0           BiocGenerics_0.24.0
##  [7] funciVar_0.1.4             ggplot2_2.2.1.9000
##  [9] ComplexHeatmap_1.17.1      knitr_1.17.20
## [11] MultiAssayExperiment_1.4.4 dplyr_0.7.4
## [13] ELMER_2.3.6                ELMER.data_2.3.2
## [15] DT_0.2
##
## loaded via a namespace (and not attached):
##   [1] shinydashboard_0.6.1          R.utils_2.6.0
##   [3] RSQLite_2.0                   AnnotationDbi_1.40.0
##   [5] htmlwidgets_0.9               BiocParallel_1.12.0
##   [7] devtools_1.13.4               DESeq_1.30.0
##   [9] munsell_0.4.3                 codetools_0.2-15
##  [11] withr_2.1.1.9000              colorspace_1.3-2
##  [13] BiocInstaller_1.28.0          Biobase_2.38.0
##  [15] highr_0.6                     rstudioapi_0.7
##  [17] labeling_0.3                  GenomeInfoDbData_1.0.0
##  [19] mnormt_1.5-5                  hwriter_1.3.2
##  [21] KMsurv_0.1-5                  bit64_0.9-7
##  [23] rprojroot_1.3-1               downloader_0.4
##  [25] biovizBase_1.26.0             ggthemes_3.4.0
##  [27] EDASeq_2.12.0                 R6_2.2.2
##  [29] doParallel_1.0.11             locfit_1.5-9.1
##  [31] AnnotationFilter_1.2.0        bitops_1.0-6
##  [33] reshape_0.8.7                 DelayedArray_0.4.1
##  [35] assertthat_0.2.0              scales_0.5.0.9000
##  [37] nnet_7.3-12                   gtable_0.2.0
##  [39] ensembldb_2.2.0               rlang_0.1.6
##  [41] genefilter_1.60.0             cmprsk_2.2-7
##  [43] GlobalOptions_0.0.12          splines_3.4.3
##  [45] rtracklayer_1.38.2            lazyeval_0.2.1
##  [47] acepack_1.4.1                 dichromat_2.0-0
##  [49] selectr_0.3-1                 broom_0.4.3
##  [51] checkmate_1.8.5               yaml_2.1.16
##  [53] reshape2_1.4.3                snpStats_1.28.0
##  [55] GenomicFeatures_1.30.0        backports_1.1.2
##  [57] httpuv_1.3.5                  Hmisc_4.0-3
##  [59] RMySQL_0.10.13                tools_3.4.3
##  [61] psych_1.7.8                   RColorBrewer_1.1-2
##  [63] Rcpp_0.12.14                  plyr_1.8.4
##  [65] base64enc_0.1-3               progress_1.1.2
##  [67] zlibbioc_1.24.0               purrr_0.2.4
##  [69] RCurl_1.95-4.8                prettyunits_1.0.2
##  [71] ggpubr_0.1.6                  rpart_4.1-11
##  [73] pbapply_1.3-3                 GetoptLong_0.1.6
##  [75] zoo_1.8-0                     SummarizedExperiment_1.8.1
##  [77] ggrepel_0.7.0                 cluster_2.0.6
##  [79] magrittr_1.5                  data.table_1.10.4-3
##  [81] circlize_0.4.3                survminer_0.4.1
##  [83] ProtGenerics_1.10.0           matrixStats_0.52.2
##  [85] aroma.light_3.8.0             hms_0.4.0
##  [87] mime_0.5                      evaluate_0.10.1
##  [89] xtable_1.8-2                  XML_3.98-1.9
##  [91] gridExtra_2.3                 shape_1.4.3
##  [93] testthat_2.0.0                compiler_3.4.3
##  [95] biomaRt_2.34.1                tibble_1.3.4
##  [97] R.oo_1.21.0                   htmltools_0.3.6
##  [99] Formula_1.2-2                 tidyr_0.7.2
## [101] geneplotter_1.56.0            DBI_0.7
## [103] matlab_1.0.2                  ShortRead_1.36.0
## [105] Matrix_1.2-12                 readr_1.1.1
## [107] R.methodsS3_1.7.1             Gviz_1.22.2
## [109] bindr_0.1                     pkgconfig_2.0.1
## [111] km.ci_0.5-2                   GenomicAlignments_1.14.1
## [113] foreign_0.8-69                plotly_4.7.1
## [115] xml2_1.1.1                    roxygen2_6.0.1
## [117] foreach_1.4.4                 annotate_1.56.1
## [119] XVector_0.18.0                rvest_0.3.2
## [121] stringr_1.2.0                 VariantAnnotation_1.24.2
## [123] digest_0.6.13                 ConsensusClusterPlus_1.42.0
## [125] Biostrings_2.46.0             rmarkdown_1.8
## [127] TCGAbiolinks_2.7.4            survMisc_0.5.4
## [129] htmlTable_1.11.0              edgeR_3.20.2
## [131] curl_3.1                      shiny_1.0.5
## [133] Rsamtools_1.30.0              commonmark_1.4
## [135] rjson_0.2.15                  nlme_3.1-131
## [137] jsonlite_1.5                  viridisLite_0.2.0
## [139] limma_3.34.4                  BSgenome_1.46.0
## [141] lattice_0.20-35               httr_1.3.1
## [143] survival_2.41-3               interactiveDisplayBase_1.16.0
## [145] glue_1.2.0                    iterators_1.0.9
## [147] bit_1.1-12                    stringi_1.1.6
## [149] blob_1.1.0                    AnnotationHub_2.10.1
## [151] latticeExtra_0.6-28           memoise_1.1.0